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Yorodumi- PDB-4l0q: Crystal structure of S-nitrosoglutathione reductase from Arabidop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l0q | ||||||
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Title | Crystal structure of S-nitrosoglutathione reductase from Arabidopsis thaliana, C370A/C373A double mutant | ||||||
Components | Alcohol dehydrogenase class-3 | ||||||
Keywords | OXIDOREDUCTASE / dimer / NADH / GSNO / alcohol dehydrogenase / homodimer / reduction of GSNO / NADH binding | ||||||
Function / homology | Function and homology information S-(hydroxymethyl)glutathione dehydrogenase / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD(P)+) activity / formaldehyde catabolic process / alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / alcohol dehydrogenase / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å | ||||||
Authors | Weichsel, A. / Crotty, J. / Montfort, W.R. | ||||||
Citation | Journal: To be Published Title: Crystal structure and kinetic behavior of alcohol dehydrogenase III/S-nitrosoglutathione reductase from Arabidopsis thaliana Authors: Crotty, J. / Greving, M. / Brettschneider, S. / Weichsel, A. / Wildner, G.F. / Vierling, E. / Montfort, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l0q.cif.gz | 166.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l0q.ent.gz | 132.3 KB | Display | PDB format |
PDBx/mmJSON format | 4l0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/4l0q ftp://data.pdbj.org/pub/pdb/validation_reports/l0/4l0q | HTTPS FTP |
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-Related structure data
Related structure data | 3ukoS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40551.363 Da / Num. of mol.: 2 / Mutation: C370A/C373A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ADH2, ADHIII, FDH1, At5g43940, MRH10.4 / Plasmid: pJC20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q96533, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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-Non-polymers , 5 types, 397 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.1 M ammonium sulfate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 18, 2006 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→28.65 Å / Num. all: 63603 / Num. obs: 63603 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.4 / Num. unique all: 6274 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3UKO Resolution: 1.95→28.65 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.262 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.184 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→28.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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